I got pregnant at the end of my 2nd year. It was a surprise. Although my husband and I had talked at length about when to have a family, we never would have chosen the middle of 3rd year to do it. However, sometimes things happen the way they are supposed to. I wouldn't change it if I could. We were also struggling with the "when do we have the 2nd baby" question, which was answered for us when we found out there were 2 babies. I tried to get as many rotations done as I could before they were born and delivered 1 1/2 weeks after I finished IM. I took 2 1/2 months off total and then finished 3rd and 4th year. I decided to take a 5th year, which was one of the best things I have ever done for myself. I have had this year to focus on my family and on some research. So much happens during the first 2-3 years of life and it was very importnant for me to be a part of that. My school (except for the chair of IM who announced to a group of >30 people that I had really poor planning and then told me I would have to repeat IM if I went into labor at any point before the final) was very supportive.
As far as interviews go, programs seem to view families either positively or negatively. You can get a sense about this by the # of residents who have babies. I was very upfront about the importance of my family and the programs that did not view this as an asset, didn't invite me for an interview. But, screw them, why would I/you want to be anywhere that didn't support me/you as a person? I'm sure that programs would view a pregnant woman in much the same way as they viewed me with 2 2 year-olds. Although I think I did not get some interviews because of the family factor, I had plenty and ended up cancelling several.
Most people will tell you that there is no good time, but there really is no bad time either. There just may not be a "best" time. Whenever it does happen, you will be able to make it work and you will receive the same excellent training that your fellow residents/classmates receive.
Sorry for my rambling.
Let me know if you have questions.
Good Luck!